1DTX | pdb_00001dtx

CRYSTAL STRUCTURE OF ALPHA-DENDROTOXIN FROM THE GREEN MAMBA VENOM AND ITS COMPARISON WITH THE STRUCTURE OF BOVINE PANCREATIC TRYPSIN INHIBITOR

• PDB DOI: https://doi.org/10.2210/pdb1DTX/pdb

• Classification: PRESYNAPTIC NEUROTOXIN
• Organism(s): Dendroaspis angusticeps
• Mutation(s): No 


• Deposited: 1991-04-29 Released: 1992-01-15 
• Deposition Author(s): Skarzynski, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 
  0.172 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Crystal structure of alpha-dendrotoxin from the green mamba venom and its comparison with the structure of bovine pancreatic trypsin inhibitor.

Skarzynski, T.

(1992) J Mol Biology 224: 671-683

• PubMed: 1373774 
• DOI: https://doi.org/10.1016/0022-2836(92)90552-u
• Primary Citation Related Structures: 
  1DTX


• PubMed Abstract: 
  

  The three-dimensional structure of alpha-dendrotoxin (alpha-DTX) from the green mamba (Dendroaspis angusticeps) venom has been determined crystallographically using the method of isomorphous replacement and refined at 2.2 A resolution using a restrained least-squares method. The crystallographic R-factor is 0.169 for all 3451 measured reflections between 7.0 and 2.2 A. Although the main-chain fold of alpha-DTX is similar to that of homologous bovine pancreatic trypsin inhibitor (BPTI), there are significant differences involving segments of the polypeptide chain close to the "antiprotease site" of BPTI. Comparison of the structure of alpha-DTX with the existing models of BPTI and its complexes with trypsin and kallikrein reveals structural differences that explain the inability of alpha-DTX to inhibit trypsin and chymotrypsin.

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Organizational Affiliation: 
• Blackett Laboratory, Imperial College, London, England.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.55 kDa 
• Atom Count: 561 
• Modeled Residue Count: 59 
• Deposited Residue Count: 59 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-DENDROTOXIN	A	59	Dendroaspis angusticeps	Mutation(s): 0
UniProt
Find proteins for P00980 (Dendroaspis angusticeps) Explore P00980  Go to UniProtKB:  P00980

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work:  0.172 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.53	α = 90
b = 39.06	β = 90
c = 23.15	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-01-15 
Deposition Author(s): Skarzynski, T.

Revision History  

• Version 1.0: 1992-01-15
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2019-12-25
  Changes: Derived calculations, Other, Polymer sequence
• Version 2.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary